Variant report

Variant	rs7857669
Chromosome Location	chr9:27032385-27032386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10738762	0.88[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap]
rs10757635	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap]
rs10812488	0.83[JPT][hapmap]
rs10812503	0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs10812507	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10812508	0.89[ASN][1000 genomes]
rs10812510	0.80[JPT][hapmap]
rs10812515	0.91[ASN][1000 genomes]
rs10812517	0.80[JPT][hapmap]
rs10812518	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[ASN][1000 genomes]
rs10812519	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10812521	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10812523	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10812525	0.83[AMR][1000 genomes]
rs10967586	0.84[JPT][hapmap]
rs10967625	0.80[TSI][hapmap]
rs10967627	0.80[JPT][hapmap]
rs10967630	0.80[JPT][hapmap]
rs10967633	0.80[JPT][hapmap]
rs10967635	0.88[CHD][hapmap];0.80[JPT][hapmap]
rs10967645	0.83[CHB][hapmap]
rs10967648	0.86[ASN][1000 genomes]
rs10967649	0.91[CHD][hapmap];0.84[JPT][hapmap]
rs10967652	0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10967661	0.85[CHD][hapmap]
rs10967662	0.80[ASN][1000 genomes]
rs10967670	0.89[ASN][1000 genomes]
rs10967672	0.83[ASN][1000 genomes]
rs10967679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10967680	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10967685	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10967704	0.81[AMR][1000 genomes]
rs10967706	0.80[AMR][1000 genomes]
rs12236850	0.88[CHD][hapmap]
rs12337896	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.85[ASN][1000 genomes]
rs12352441	0.80[TSI][hapmap]
rs1541144	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1577328	0.89[CHB][hapmap]
rs1591355	0.82[AMR][1000 genomes]
rs1819539	0.89[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs2095405	0.84[AMR][1000 genomes]
rs2225720	0.83[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs3739544	0.80[JPT][hapmap]
rs3739547	0.91[CHD][hapmap]
rs3758218	0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs4413873	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs4463511	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4621911	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6475945	0.94[JPT][hapmap]
rs6475954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6475955	0.85[AMR][1000 genomes]
rs7018585	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7020010	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs7030567	0.85[AMR][1000 genomes]
rs7035447	0.88[CHD][hapmap];0.80[JPT][hapmap]
rs7038218	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7040505	0.83[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs7042447	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7045747	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7849248	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs7854191	1.00[ASN][1000 genomes]
rs7856462	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs7857447	0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs7860542	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7863476	0.88[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap]
rs7868158	0.94[JPT][hapmap];0.94[MEX][hapmap]
rs7870787	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs7871668	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7872496	0.84[JPT][hapmap]
rs7873073	0.90[CHD][hapmap]
rs7874940	0.80[JPT][hapmap]
rs7875068	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7875171	0.80[JPT][hapmap]
rs9644870	0.91[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv3427395	chr9:27025338-27040548	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv466334	chr9:27028947-27098940	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv613944	chr9:27028947-27098940	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7857669	IFT74	cis	lymphoblastoid	seeQTL
rs7857669	IFT74	cis	parietal	SCAN
rs7857669	FAM180A	trans	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26957200-27040000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr9:26985200-27063800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr9:26991800-27058000	Weak transcription	NHDF-Ad	bronchial
4	chr9:27009800-27070000	Weak transcription	Psoas Muscle	Psoas
5	chr9:27011200-27037400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr9:27012000-27048800	Weak transcription	HepG2	liver
7	chr9:27014400-27060800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr9:27014400-27068200	Weak transcription	Fetal Heart	heart
9	chr9:27018400-27065200	Weak transcription	Osteobl	bone
10	chr9:27019200-27061800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr9:27022600-27036200	Weak transcription	NHEK	skin
12	chr9:27024400-27047200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr9:27024400-27053800	Weak transcription	Lung	lung
14	chr9:27024400-27082600	Weak transcription	Gastric	stomach
15	chr9:27024600-27036200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:27024600-27036400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:27024600-27037400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr9:27024600-27037600	Weak transcription	HSMMtube	muscle
19	chr9:27024600-27044800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:27024600-27048600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr9:27024600-27048800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:27024600-27049200	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:27024600-27053400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:27024600-27054400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:27024600-27056400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr9:27024600-27058800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr9:27024600-27059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:27024600-27061000	Weak transcription	Dnd41	blood
29	chr9:27024600-27061400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:27024600-27061800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:27024600-27064400	Weak transcription	Colonic Mucosa	Colon
32	chr9:27024600-27075800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:27024600-27078600	Weak transcription	Aorta	Aorta
34	chr9:27024600-27079000	Weak transcription	Pancreas	Pancrea
35	chr9:27024600-27082400	Weak transcription	Primary T cells from cord blood	blood
36	chr9:27024600-27083400	Weak transcription	Left Ventricle	heart
37	chr9:27024600-27085000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr9:27024600-27086800	Weak transcription	Right Ventricle	heart
39	chr9:27024800-27033400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr9:27024800-27033600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr9:27024800-27034600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:27024800-27037400	Weak transcription	Adipose Nuclei	Adipose
43	chr9:27024800-27044800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:27024800-27048600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:27024800-27048800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr9:27024800-27048800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:27024800-27048800	Weak transcription	Thymus	Thymus
48	chr9:27024800-27050600	Weak transcription	Spleen	Spleen
49	chr9:27024800-27056800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:27024800-27058200	Weak transcription	Fetal Brain Male	brain

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